How are you interpreting "within 4A of my protein?" What has your protein's center of mass got to do with it?
Mark On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > Yes it is. So that means I need a cut-off greater than right? > > Akash > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:08 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Is the radius of your protein greater than 0.4 nm? > > Mark > > On Wed, 28 Jun 2017 12:05 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > > > Hi, > > > > I want to select all the ligands in my box within 4A of my protein. I > > looked at gmx help select and I used the command below but nothing > > appeared. It didn't show my default groups which correspond to the > > "14" for ligand and "1" for protein. Please advise me on what to do? > > Am I missing something? > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 10000 -tu ns -select `group > > "14" and within 0.4 of com of group "1"' > > > > Many thanks, > > > > Akash > > > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 21 June 2017 11:56 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Hi, > > > > You aren't getting output because you aren't actually making a > > selection - see "gmx help select" and its suggestions for where to > > look for the rest of the documentation and explained examples. > > > > Mark > > > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > <akash.pandya...@ucl.ac.uk> > > wrote: > > > > > I'm not sure if the command I entered (shown below) is correct. No > > > output was given. I'm unclear as to how this command will enable me > > > to isolate the glycine molecules within 4A of the protein molecule? > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > > > Akash > > > > > > -----Original Message----- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > > Abraham > > > Sent: 16 June 2017 17:22 > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > Hi, > > > > > > Gmx select will produce a selection eg of all molecules with an atom > > > within a cutoff of any atom in another molecule. > > > > > > Mark > > > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk> > > wrote: > > > > > > > Hi all, > > > > > > > > I have ran a simulation with a protein and multiple ligand > > > > molecules inserted randomly inside a box. I want to isolate those > > > > ligand molecules that are closest to the protein by a cut-off of > > > > four angstroms or so. Is there a command I could use to do this > > > > for me or would I have to use a molecular visualizer software for > this? > > > > > > > > Thanks, > > > > > > > > Akash > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? 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Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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